Cloning and sequencing of the matrix protein (M) gene of turkey rhinotracheitis virus reveal a gene order different from that of respiratory syncytial virus

Abstract

Several biochemical properties and the sequence of the fusion glycoprotein (F) have indicated that turkey rhinotracheitis virus (TRTV) is a pneumovirus, subfamily Pneumovirinae of the Paramyxoviridae family. As TRTV was known to generate polycistronic mRNAs, cDNA was generated from TRTV strain UK/3BV/85-infected Vero cell mRNAs using an oligonucleotide primer corresponding to a region of the F gene. Sequencing of four cDNAs revealed that the gene adjacent to the beginning (3' end) of the F gene was that for the matrix (M) protein, i.e., that TRTV had the partial gene order 3'-M-F-5'. This was unexpected as human respiratory syncytial (RS) virus, the type species of the genus Pneumovirus, has the partial gene order 3'-M-SH-G-F-5', where SH and G are the small hydrophobic protein and attachment glycoprotein, respectively. Instead TRTV resembled the Morbillivirus and Paramyxovirus genera of the Paramyxoviridae (subfamily Paramyxovirinae) which have the partial gene order 3'-M-F-5'. Two further oligonucleotides, one corresponding to a sequence near the end of the M gene and the other (oligo B) to a sequence near the beginning of the F gene, with their 5' ends spaced 300 nucleotides apart on the basis of the cDNA sequence, were used in a polymerase chain reaction (PCR) using genomic RNA as template. Only a PCR product of 0.3 kb was obtained. The same sized product was also obtained using these oligonucleotides and genomic RNA from three other TRTV strains (SA/91/78, UK/8544/85, and SA/2381/88) which had been grown in chicken tracheal organ cultures. In addition PCR was performed using genomic RNA from TRTV-3BV and SA/2381/88 with oligo B and another oligonucleotide near the 5' end of the gene upstream from M, spaced 1141 nucleotides apart on the basis of the sequence data. Only a 1.14-kb PCR product was obtained. Larger products would have been expected if another gene had been situated between M and F. The absence of such larger products, plus the demonstration that infected cells contained M-F dicistronic mRNAs, supported the conclusion that in the TRTV genome the M gene is adjacent to the F gene in the order 3'-M-F-5'. The 5' termini of the M and F mRNAs were confirmed by mRNA mapping. The TRTV M gene encoded a protein of 254 amino acids, very similar to that of RS virus (256 residues; 37% amino acid identity) but very different from that of the morbilliviruses and paramyxoviruses (approximately 350 residues).(ABSTRACT TRUNCATED AT 400 WORDS)

Sequence analysis of the 22K, SH and G genes of turkey rhinotracheitis virus and their intergenic regions reveals a gene order different from that of other pneumoviruses

“…This has been supported by comparison of the inferred F and matrix (M) protein sequences with those of RSV and several paramyxoviruses and morbilliviruses (Yu et al, 1991(Yu et al, , 1992. The identification of a 22K gene also supports this assignment.…”

“…The sequences at the 5' ends of TRTV mRNAs appear to be highly conserved, the first nine nucleotides of the three genes described here and those of the F and M genes reported by Yu et al (1991Yu et al ( , 1992 being identical (GGGACAAGU). The gene start signals of other TRTV genes are probably also highly similar because the primer corresponding to the first 16 nucleotides of the SH gene amplified sequences from three other TRTV genes in addition to the SH gene.…”

“…However, the genome of TRTV differs significantly from those of the two other pneumoviruses that have been studied at the sequence level. The F gene has been shown to be located adjacent to the M gene rather than the G gene as in RSV (3' M-F 5" in TRTV compared with 3' M-SH-G-F 5"; Yu et al, 1992). The data presented here show that the gene order in TRTV is 3' F-22K-SH-G 5' rather than 3' SH-G-F-22K 5', observed in RSV and PVM.…”

Subgroup C avian metapneumovirus (MPV) and the recently isolated human MPV exhibit a common organization but have extensive sequence divergence in their putative SH and G genes

“…First reported in the late 1970s in South Africa (Buys & Du Preez, 1980), and subsequently in France and the UK (Giraud et al, 1986;McDougall & Cook, 1986), APVs have now been described worldwide, although Australia is still considered to be free from infection (Bell & Alexander, 1990). APV has been proposed as the type species for the newly defined genus Metapneumovirus (Pringle, 1998), which was created within the subfamily Pneumovirinae to account for the APV genome containing eight genes arranged in the order 39-N-P-M-F-M2-SH-G-L-59, instead of 10 genes arranged in the order 39-NS1-NS2-N-P-M-SH-G-F-M2-L-59, as found in pneumoviruses from mammals, such as respiratory syncytial virus (RSV) (Yu et al, 1992).…”

Complete sequence of the G glycoprotein gene of avian metapneumovirus subgroup C and identification of a divergent domain in the predicted protein

“…The virus contains a non-segmented, singlestranded, negative-sense RNA genome with the gene order 39-le-N-P-M-F-M2-SH-G-L-tr-59 (Ling & Pringle, 1988;Yu et al, 1992). The nucleotide sequences of all eight genes of AMPV-A have been determined (Randhawa et al, 1997 and references therein).…”